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Sodium in PDB 6efc: Hsa Siglec + Unique Domains (Unliganded)

Protein crystallography data

The structure of Hsa Siglec + Unique Domains (Unliganded), PDB code: 6efc was solved by T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.45 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.635, 58.173, 75.973, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17.9

Other elements in 6efc:

The structure of Hsa Siglec + Unique Domains (Unliganded) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Hsa Siglec + Unique Domains (Unliganded) (pdb code 6efc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Hsa Siglec + Unique Domains (Unliganded), PDB code: 6efc:

Sodium binding site 1 out of 1 in 6efc

Go back to Sodium Binding Sites List in 6efc
Sodium binding site 1 out of 1 in the Hsa Siglec + Unique Domains (Unliganded)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hsa Siglec + Unique Domains (Unliganded) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:27.8
occ:1.00
O A:TYR377 2.2 28.9 1.0
O A:HOH820 2.2 43.3 1.0
O A:ASN374 2.3 25.4 1.0
O A:HOH830 2.4 43.1 1.0
OD2 A:ASP436 2.4 30.9 1.0
OD1 A:ASP436 2.7 32.4 1.0
CG A:ASP436 2.9 30.8 1.0
HD3 A:PRO379 3.3 33.9 1.0
C A:ASN374 3.3 23.8 1.0
C A:TYR377 3.4 25.9 1.0
HB2 A:ASN374 3.5 29.3 1.0
H A:TYR377 3.6 25.3 1.0
HA A:GLU375 3.6 28.9 1.0
HA A:ASP378 3.7 32.6 0.5
HA A:ASP378 3.7 32.2 0.5
HB2 A:TYR377 4.0 27.1 1.0
HH A:TYR430 4.0 29.2 1.0
HD2 A:PRO379 4.1 33.9 1.0
CD A:PRO379 4.1 28.3 1.0
HA A:ASN374 4.1 27.3 1.0
CA A:ASN374 4.1 22.8 1.0
N A:GLU375 4.2 23.4 1.0
CB A:ASN374 4.2 24.4 1.0
N A:TYR377 4.2 21.1 1.0
CA A:TYR377 4.3 22.9 1.0
CA A:GLU375 4.3 24.1 1.0
OD1 A:ASP378 4.3 34.3 0.5
CB A:ASP436 4.3 28.3 1.0
N A:ASP378 4.3 26.1 1.0
CA A:ASP378 4.5 26.9 0.5
CA A:ASP378 4.5 27.2 0.5
OH A:TYR430 4.5 24.3 1.0
HB3 A:ASP436 4.5 33.9 1.0
CB A:TYR377 4.6 22.6 1.0
C A:GLU375 4.6 23.4 1.0
HB2 A:ASP436 4.7 33.9 1.0
HE2 A:TYR430 4.8 25.6 1.0
HG2 A:PRO379 4.8 36.0 1.0
CG A:PRO379 4.9 30.0 1.0
O A:GLU375 4.9 24.6 1.0
HG3 A:PRO379 4.9 36.0 1.0
HB3 A:TYR377 5.0 27.1 1.0
CG A:ASN374 5.0 24.2 1.0
HB3 A:ASN374 5.0 29.3 1.0
H A:GLU375 5.0 28.1 1.0

Reference:

T.M.Iverson, T.M.Iverson. N/A N/A.
Page generated: Tue Dec 15 12:10:41 2020

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